Centers for Disease Control and Prevention

National Center for Immunization and Respiratory Diseases

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Current landscape of SARS-CoV-2 lineages

September 2023

Natalie J. Thornburg, PhD

Chief, Laboratory Branch

Coronaviruses and Other Respiratory Viruses Division
Trends in weighted lineage proportion estimates & Nowcast 

United States, May 27 – September 2, 2023

https://covid.cdc.gov/covid-data-tracker/#variant-proportions Accessed 9/1/2023

Two-week period ending
Convergent Evolution of Different Omicron Sub-lineages:

Key changes in the spike receptor binding domain (RBD) detected since September 2022

Lineage

Spike RBD (residues 333-527) amino acid substitutions

339

§

346

§,¶

368 444

§,¶

445

¶

446

§,¶

452

§,¶

460

§,¶

478 486

§,¶

490

§,¶

521

Reference sequence: BA.4/BA.5 D R L K V G R N K V F P

BA.4.6, BA.5.2.6, BF.7, BF.11 — T — — — — — — — — — —

BQ.1 — — — T — — — K — — — —

BQ.1.1 — T — T — — — K — — — —

BA.2.75 H — — — — S L K — F — —

BN.1 H T — — — S L K — F S —

CH.1.1 H T — T — S — K — S — —

XBB, XBB.1 H T I — P S L K — S S —

XBB.1.5, XBB.1.5.1, FD.2, XBB.1.9.1, 

XBB.1.9.2

H T I — P S L K — P S —

XBB.1.16, XBB.1.16.1 H T I — P S L K R P S —

XBB.2.3 H T I — P S L K — P S S

Ma et al. MMWR to be published on June 15, 2023

§

Indicates sites of independent substitutions in at least two different evolutionary lineages.

¶

Indicates sites identified in a previous study associated with in vitro reductions in binding by monoclonal antibodies that were previously FDA-authorized.

Bolded sub-lineages are expanding in the United States as of June 10, 2023
More than 90% of circulating viruses have similar Spike receptor 

binding domain sequences

Lineage

Spike RBD (residues 333-527) amino acid substitutions

452 455 456 460 478 486 521

Reference sequence: XBB.1.5 L L F K K P P

XBB.1.9 — — — — — S —

XBB.1.5.70 — F L — — — —

XBB.1.16 — — — — R — —

EG, FL — — L — — — —

EG.5, EG.5.1.6, FL.1.5 — — L — — — —

XBB.1.16.6, XBB.1.16.9, FL.1.5.1, HN.1 — — L — R — —

HV.1 R — L — — — —

HK.3 — F L — — — —

XBB.2.3 — — — — — — S

XBB.1.16, XBB.1.16.1 — — — — R — —
XBB.1.5 and XBB.1.16 Spike substitutions relative to 

BA.5

Receptor 

binding motif

Receptor 

binding domain

N-terminal 

domain

Remainder of 

S1

S2

ACE2 ACE2

XBB.1.5 XBB.1.16
BA.2.86 is a descendent of BA.2

Nexstrain (Roemer / Neher)

• Most closely related 

to BA.2

• BA.2 and its lineages 

circulated in spring 

2022 before BA.5 

viruses
BA.2.86 has >30 amino acid substitions in spike in 

comparison to XBB.1.5

▪ >30 amino acid substitutions in Spike in comparison to XBB.1.5

– Variation between sequences due to missing data and sequencing artifacts

▪ First detected in specimen collected in late July, 2023

▪ As of 9/6 detected in 7 clinical specimens in 7 US states and 1 additional state in 

waste water

▪ Detected in 10 countries

▪ Small number of sequences 
Reduction in pseudovirus neutralization is not detected 

using sera from people infected with XBB lineage 

viruses

Qian Wang 

Dr. David D. Ho lab
No reduction in BA.2.86 pseudovirus neutralization 

is observed after bivalent vaccination, or after 6 

months with or without XBB infection

Lasrado et al. Neutralization Escape by SARS-CoV-2 Omicron Subvariant BA.2.86 | bioRxiv
Data generation with authentic viruses

▪ More than 90% of currently circulating viruses are XBB lineage viruses with 1-2 

additional substitutions in RBD in comparison to XBB.1.5

▪ BA.2.86 is a newly detected lineage with > 30 amino acid substitutions in spike

– Thus far, the number of viruses detected is still low

– Sequence numbers are too low to calculate proportion (<0.05%)

▪ Preliminary pseudovirus neutralization data generated by multiple labs do not 

indicate a large reduction in neutralizing activity against BA.2.86

▪ CDC has generated a BA.2.86 isolates, is currently working on titrations before 

neutralization and will distribute to external laboratories for further examination
▪ More than 90% of currently circulating viruses are XBB lineage viruses with 1-2 

additional substitutions in RBD in comparison to XBB.1.5

▪ BA.2.86 is a newly detected lineage with > 30 amino acid substitutions in spike

– Thus far, the number of viruses detected is still low

– Sequence numbers are too low to calculate proportion (<0.05%)

▪ Preliminary pseudovirus neutralization data generated by multiple labs do not 

indicate a large reduction in neutralizing activity against BA.2.86

▪ CDC has generated a BA.2.86 isolate, is currently working on titrations before 

neutralization and has begun distribution to external laboratories for further 

examination

Summary
For more information, contact CDC

1-800-CDC-INFO (232-4636)

TTY: 1-888-232-6348 www.cdc.gov

The findings and conclusions in this report are those of the authors and do not necessarily represent the official 

position of the Centers for Disease Control and Prevention.

Photographs and images included in this presentation are licensed solely for CDC/NCIRD online and presentation 

use. No rights are implied or extended for use in printing or any use by other CDC CIOs or any external audiences.